From fe45deb3baa12c65d14c3853c614012e1a3c18cf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ant=C3=B3nio=20Paulo?= <antonio.do.paulo@ist.utl.pt>
Date: Sun, 28 Jul 2019 20:44:29 +0200
Subject: [PATCH] update MuTect2 with gatk 4.1.2.0 inputs
The "--f1r2-tar-gz" input is used in FilterMutectCalls (check: https://gatkforums.broadinstitute.org/gatk/discussion/24057/how-to-call-somatic-mutations-using-gatk4-mutect2#latest).
The "---germline-resource" input was already available in gatk 4.1.0.0.
---
gatk.wdl | 8 +++++++-
1 file changed, 7 insertions(+), 1 deletion(-)
diff --git a/gatk.wdl b/gatk.wdl
index 020adc7..578765b 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -258,13 +258,16 @@ task MuTect2 {
String outputVcf
String tumorSample
String? normalSample
+ File? germlineResource
+ File? germlineResourceIndex
File? panelOfNormals
File? panelOfNormalsIndex
+ String? f1r2TarGz = "f1r2.tar.gz"
Array[File]+ intervals
Int memory = 4
Float memoryMultiplier = 3
- String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
}
command {
@@ -276,7 +279,9 @@ task MuTect2 {
-I ~{sep=" -I " inputBams} \
-tumor ~{tumorSample} \
~{"-normal " + normalSample} \
+ ~{"--germline-resource " + germlineResource} \
~{"--panel-of-normals " + panelOfNormals} \
+ ~{"--f1r2-tar-gz " + f1r2TarGz} \
-O ~{outputVcf} \
-L ~{sep=" -L " intervals}
}
@@ -284,6 +289,7 @@ task MuTect2 {
output {
File vcfFile = outputVcf
File vcfFileIndex = outputVcf + ".tbi"
+ File f1r2File = f1r2TarGz
}
runtime {
--
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